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GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

# error message: -3

Member Posts: 1
edited January 2013

hello
I am a new user of GATK, until now I found the answer to my questions on your forum. Following is the command "java -jar ../GATK/GenomeAnalysisTK.jar -T BaseRecalibrator -I 9485_realignedBam.fixed.bam -R hg19.fa -knownSites dbsnp_132_hg19.vcf -o recal_data.grp -filterMBQ" from wich I get this error message :

# # # # # ERROR stack trace
java.lang.ArrayIndexOutOfBoundsException: -3
at
at
at
at
# # # # # ERROR -------------------------------------------- ----------------------------------------------
# # # # # ERROR A RUNTIME ERROR GATK has occurred (version 2.3-6-gebbba25)
# # # # # ERROR
# # # # # ERROR Please visit the wiki to see if this is a known problem
# # # # # ERROR If not, please post the error, with stack trace to the forum GATK
# # # # # ERROR Visit our website and forum for extensive documentation and answers to
# # # # # ERROR
# # # # # ERROR MESSAGE: -3
# # # # # ERROR --------------------
`

I can not find it on a forum, can you explain it and help me

thank you

Post edited by Geraldine_VdAuwera on
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